The World Cup dreams of Conor Washington and Oliver Norwood were dashed as they played out a 0-0 draw with Switzerland in Basel.
The QPR and Fulham stars both started for Northern Ireland who were unable to overcome the one-goal deficit from the first leg, as the controversial hand-ball decision from the first leg proved an unfortunate decider.
The hosts started the stronger of the two teams and could have taken an early lead when Xherdan Shaqiri swung a free-kick into the area only for Gareth McAuley to make a list-ditch clearance.
The Stoke City man looked dangerous whenever he got on the ball, and seemed the most likely to make something happen in the first period.
Northern Ireland kept the game tight, and came close through two Chris Brunt chances, as well as an opportunity for Washington, who headed just wide after great work from Jamie Ward.
Both sides had chances in the second half, including a header from Jonny Evans which was cleared off the line in injury time, but it wasn't to be for Michael O'Neill's side, who will be left with a bitter taste in their mouth as they are eliminated in the most acrimonious circumstances.